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Yorodumi- PDB-7bq2: X-ray structure of human PPARalpha ligand binding domain-pemafibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bq2 | ||||||
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Title | X-ray structure of human PPARalpha ligand binding domain-pemafibrate-SRC1 coactivator peptide co-crystals obtained by soaking | ||||||
Components |
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Keywords | TRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR | ||||||
Function / homology | Function and homology information positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / regulation of fatty acid metabolic process / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / regulation of fatty acid metabolic process / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / labyrinthine layer morphogenesis / ubiquitin conjugating enzyme binding / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / negative regulation of glycolytic process / positive regulation of female receptivity / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / nitric oxide metabolic process / positive regulation of fatty acid metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NFAT protein binding / positive regulation of ATP biosynthetic process / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / cellular response to Thyroglobulin triiodothyronine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / estrous cycle / phosphatase binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / negative regulation of reactive oxygen species biosynthetic process / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of gluconeogenesis / negative regulation of signaling receptor activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / MDM2/MDM4 family protein binding / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / negative regulation of blood pressure / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cellular response to starvation / regulation of cellular response to insulin stimulus / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / hippocampus development / gluconeogenesis / response to progesterone / fatty acid metabolic process / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / wound healing / SUMOylation of intracellular receptors / Heme signaling / response to insulin / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å | ||||||
Authors | Kamata, S. / Ishikawa, R. / Akahane, M. / Oyama, T. / Ishii, I. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Iscience / Year: 2020 Title: PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Authors: Kamata, S. / Oyama, T. / Saito, K. / Honda, A. / Yamamoto, Y. / Suda, K. / Ishikawa, R. / Itoh, T. / Watanabe, Y. / Shibata, T. / Uchida, K. / Suematsu, M. / Ishii, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bq2.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bq2.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bq2_validation.pdf.gz | 746.4 KB | Display | wwPDB validaton report |
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Full document | 7bq2_full_validation.pdf.gz | 751.6 KB | Display | |
Data in XML | 7bq2_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7bq2_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/7bq2 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/7bq2 | HTTPS FTP |
-Related structure data
Related structure data | 6kaxC 6kayC 6kazC 6kb0C 6kb1C 6kb2C 6kb3C 6kb4C 6kb5C 6kb6C 6kb7C 6kb8C 6kb9C 6kbaC 6kypC 6l36C 6l37C 6l38C 6lx4C 6lx5C 6lx6C 6lx7C 6lx8C 6lx9C 6lxaC 6lxbC 6lxcC 7bpyC 7bpzC 7bq0C 7bq1C 7bq3C 7bq4C 3sp6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30856.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869 |
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#2: Protein/peptide | Mass: 1848.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase |
#3: Chemical | ChemComp-P7F / ( |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1M Tris (pH 8.0), 25%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020 / Details: Mirrors | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.52→43 Å / Num. obs: 42160 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 16 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SP6 Resolution: 1.52→32.847 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.61 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.63 Å2 / Biso mean: 23.1362 Å2 / Biso min: 10.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→32.847 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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